HIV-associated nephropathy (HIVAN) is a leading cause of end stage kidney disease among African-Americans. Despite growing knowledge of the disease mechanism, therapeutic options have been limited. While gene expression microarray has been widely applied for the study of kidney diseases, data analytical tools are quite limited. Here we propose a novel approach to link the microarray data to the upstream signaling kinase activation using computation/systems biology approach. To accomplish this, we have developed several computational programs including Gene2 Network, a system that uses protein-protein interactions and cell signaling networks to build subnetworks based on seed lists of genes, and kinase enrichment analysis (KEA), a tool that links lists of proteins to the kinases most likely regulating their activity. Using this approach to study the kidney disease in a HIV-1 transgenic mouse model (Tg26 mice), which is a well-characterized animal model for human HIVAN, we identified that homeodomain interacting protein kinase 2 (HIPK2) is a novel upstream kinase regulating the transcription factors and genes activated in kidneys of Tg26 mice. HIPK2 is known to be involved in the regulation of p53, TGF-2, Wnt/2-catenin, and Notch pathways, which are known to mediate apoptosis and fibrosis in kidney disease including HIVAN. Our preliminary data suggest that HIPK2 protein expression is increased markedly in the renal tubulo-interstitial compartment of Tg26 mice and human with HIVAN. In addition, HIPK2 mediates HIV-induced apoptosis and epithelial-mesenchymal transition (EMT) of renal tubular epithelia cells, contributing to kidney fibrosis. Based on these preliminary data we hypothesize that HIPK2 is an upstream protein kinase that mediates tubulointersitial injury in HIVAN and in other kidney diseases. To test our hypotheses, we propose the following specific aims: Specific aim 1: Examine the role of HIPK2 in vitro by confirming the role of HIPK2 in apoptosis and EMT of HIV-infected cells and by determining signaling pathways up- and down-stream of HIPK2 that are activated by HIV. Specific aim 2: Confirm the role of HIPK2 in vivo by investigating whether HIPK2 knockout mice are protected from the development of tubulointerstitial injury in the unilateral ureteral obstruction model and by assessing the effect of HIPK2 knockout on the development of tubulointerstitial injury in Tg26. PUBLIC HEALTH RELEVANCE: HIPK2 could be a novel upstream kinase activating multiple downstream pathways leading to tubulo-interstitial injury, which is a final common pathway in the progression of chronic kidney disease. HIPK2 could be a potential new therapeutic target for the treatment of HIV-associated nephropathy as well as other kidney diseases. Our studies will also provide a novel approach to link upstream signaling pathways to data from gene expression microarray, which could help us to identify key upstream kinases responsible for kidney injury in HIVAN, as well as in other diseases.